[English] 日本語
Yorodumi
- PDB-9k3q: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k3q
TitleCryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Components
  • (Light-harvesting protein B-870 ...) x 2
  • (Reaction center protein ...) x 2
  • Photoreaction center protein H
KeywordsPHOTOSYNTHESIS / reaction centre light-harvesting 1
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / metal ion binding / membrane / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Trans-Geranyl BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / Reaction center protein L chain / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu, Z.K. / Wang, P. / Liu, L.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Authors: Liu, Z.K. / Wang, P. / Liu, L.N.
History
DepositionOct 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Light-harvesting protein B-870 beta chain
2: Light-harvesting protein B-870 alpha chain
3: Light-harvesting protein B-870 beta chain
4: Light-harvesting protein B-870 alpha chain
5: Light-harvesting protein B-870 beta chain
6: Light-harvesting protein B-870 alpha chain
7: Light-harvesting protein B-870 beta chain
8: Light-harvesting protein B-870 alpha chain
9: Light-harvesting protein B-870 beta chain
A: Light-harvesting protein B-870 alpha chain
D: Light-harvesting protein B-870 alpha chain
E: Light-harvesting protein B-870 alpha chain
F: Light-harvesting protein B-870 alpha chain
G: Light-harvesting protein B-870 alpha chain
H: Photoreaction center protein H
I: Light-harvesting protein B-870 beta chain
J: Light-harvesting protein B-870 alpha chain
K: Light-harvesting protein B-870 beta chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Light-harvesting protein B-870 alpha chain
O: Light-harvesting protein B-870 beta chain
Q: Light-harvesting protein B-870 beta chain
R: Light-harvesting protein B-870 alpha chain
S: Light-harvesting protein B-870 beta chain
T: Light-harvesting protein B-870 alpha chain
U: Light-harvesting protein B-870 beta chain
V: Light-harvesting protein B-870 alpha chain
W: Light-harvesting protein B-870 beta chain
X: Light-harvesting protein B-870 alpha chain
Y: Light-harvesting protein B-870 beta chain
Z: Light-harvesting protein B-870 alpha chain
d: Light-harvesting protein B-870 beta chain
m: Light-harvesting protein B-870 beta chain
n: Light-harvesting protein B-870 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,81295
Polymers252,88735
Non-polymers47,92560
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Light-harvesting protein B-870 ... , 2 types, 32 molecules 13579IKOQSUWYdmn2468ADEFGJNRTVXZ

#1: Protein/peptide
Light-harvesting protein B-870 beta chain / Antenna pigment protein beta chain / LH-1


Mass: 5037.832 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P0C190
#2: Protein/peptide
Light-harvesting protein B-870 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 5308.227 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P02947

-
Protein , 1 types, 1 molecules H

#3: Protein Photoreaction center protein H


Mass: 27745.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: Q7M149

-
Reaction center protein ... , 2 types, 2 molecules LM

#4: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30472.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pufL / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P10717
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 29131.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A2974 / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: Q2RQ26

-
Non-polymers , 5 types, 60 molecules

#6: Chemical...
ChemComp-07D / Trans-Geranyl BACTERIOCHLOROPHYLL A


Mass: 901.425 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C55H64MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97584 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00622452
ELECTRON MICROSCOPYf_angle_d0.86531078
ELECTRON MICROSCOPYf_dihedral_angle_d11.6354991
ELECTRON MICROSCOPYf_chiral_restr0.0382820
ELECTRON MICROSCOPYf_plane_restr0.0064575

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more